Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
CryptShovingCaBasedDivisionRule.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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10This file is part of Chaste.
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12Redistribution and use in source and binary forms, with or without
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14 * Redistributions of source code must retain the above copyright notice,
15 this list of conditions and the following disclaimer.
16 * Redistributions in binary form must reproduce the above copyright notice,
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19 * Neither the name of the University of Oxford nor the names of its
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21 software without specific prior written permission.
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23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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32OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33
34*/
35
36#include "CryptShovingCaBasedDivisionRule.hpp"
37#include "RandomNumberGenerator.hpp"
38#include "StemCellProliferativeType.hpp"
39
41{
42 std::set<unsigned> neighbouring_node_indices = pPottsMesh->GetVonNeumannNeighbouringNodeIndices(NodeIndex);
43 unsigned num_neighbours = neighbouring_node_indices.size();
44
45 // No strange neighbourhoods and in 2D so need 3 or 4 neighbours
46 if (num_neighbours == 4)
47 {
48 return true;
49 }
50 else if (num_neighbours == 3)
51 {
52 // Quick and dirty check to see if cells are in bottom or top half of the domain
53 if (NodeIndex < 0.5*pPottsMesh->GetNumNodes())
54 {
55 return false;
56 }
57 else
58 {
59 EXCEPTION("Cells reaching the top of the crypt need to increase length to at least double the sloughing height.");
60 }
61 }
62 else
63 {
64 // If here then have <2 or >4 neighbours and not possible for 2d periodic crypt
66 }
67}
68
70{
71 return true;
72}
73
75 CellPtr pParentCell,
76 CaBasedCellPopulation<2>& rCellPopulation)
77{
78 // Get node index corresponding to the parent cell
79 unsigned parent_node_index = rCellPopulation.GetLocationIndexUsingCell(pParentCell);
80
81 PottsMesh<2>* static_cast_mesh = static_cast<PottsMesh<2>*>(&(rCellPopulation.rGetMesh()));
82
83 // This tracks if the cell is on the base of the crypt, and offsets the neighbours accordingly
84 bool is_not_on_base = IsNodeOnBase(parent_node_index,static_cast_mesh);
85
86 /*
87 * Select a neighbour at random.
88 * Sample random number to specify which move to make either 1 (E) 2 (W) or 3 (N)
89 * This is as they are ordered in node index and that moves from south west to north east.
90 */
92 unsigned direction = p_gen->randMod(3)+ (unsigned) is_not_on_base;
93
94 // Stem Cells only divide vertically
95 if (pParentCell->GetCellProliferativeType()->IsType<StemCellProliferativeType>())
96 {
97 direction = 2;
98 }
99
100
101 std::set<unsigned> neighbouring_node_indices = static_cast_mesh->GetVonNeumannNeighbouringNodeIndices(parent_node_index);
102
103 std::set<unsigned>::iterator neighbour_iter = neighbouring_node_indices.begin();
104 for (unsigned i=0; i<direction; i++)
105 {
106 ++neighbour_iter;
107 }
108 assert(neighbour_iter != neighbouring_node_indices.end());
109
110 unsigned daughter_node_index = *neighbour_iter;
111
112 assert(daughter_node_index < static_cast_mesh->GetNumNodes());
113
114 // If daughter node is occupied then move the cell north (which is always the last one in the set of neighbours)
115 if (!(rCellPopulation.IsSiteAvailable(daughter_node_index, pNewCell)))
116 {
117 std::list<std::pair<unsigned,unsigned> > cell_moves;
118
119 bool is_neighbour_occupied = true;
120
121 unsigned current_node_index = parent_node_index;
122 unsigned target_node_index = daughter_node_index;
123 while (is_neighbour_occupied)
124 {
125 current_node_index = target_node_index;
126
127 std::set<unsigned> neighbouring_node_indices = static_cast_mesh->GetVonNeumannNeighbouringNodeIndices(current_node_index);
128 unsigned num_neighbours = neighbouring_node_indices.size();
129
130 // Check to see if the current node is on the boundary
131 IsNodeOnBase(current_node_index, static_cast_mesh);
132
133 // Select the appropriate neighbour
134 std::set<unsigned>::iterator neighbour_iter = neighbouring_node_indices.begin();
135 for (unsigned i=0; i<num_neighbours-1; i++)
136 {
137 ++neighbour_iter;
138 }
139 assert(neighbour_iter != neighbouring_node_indices.end());
140
141 target_node_index = *neighbour_iter;
142
143 std::pair<unsigned, unsigned> new_move(current_node_index, target_node_index);
144
145 cell_moves.push_back(new_move);
146
147 // If target node is unoccupied move the cell on the current node to the target node and stop shoving cells
148 if (rCellPopulation.IsSiteAvailable(target_node_index, pNewCell))
149 {
150 is_neighbour_occupied = false;
151 }
152
153 // If target node is occupied then keep shoving the cells out of the way
154 current_node_index = target_node_index;
155 }
156
157 // Do moves to free up the daughter node index
158 for (std::list<std::pair<unsigned, unsigned> >::reverse_iterator reverse_iter = cell_moves.rbegin();
159 reverse_iter != cell_moves.rend();
160 ++reverse_iter)
161 {
162 assert(rCellPopulation.IsSiteAvailable(reverse_iter->second, pNewCell));
163 assert(!(rCellPopulation.IsSiteAvailable(reverse_iter->first, pNewCell)));
164
165 // Move cell from first() to second()
166 rCellPopulation.MoveCellInLocationMap(rCellPopulation.GetCellUsingLocationIndex(reverse_iter->first), reverse_iter->first, reverse_iter->second);
167 }
168
169 // Check daughter site is now free
170 assert(rCellPopulation.IsSiteAvailable(daughter_node_index, pNewCell));
171
172 }
173 return daughter_node_index;
174}
175
176// Serialization for Boost >= 1.36
#define EXCEPTION(message)
#define NEVER_REACHED
#define CHASTE_CLASS_EXPORT(T)
unsigned GetLocationIndexUsingCell(CellPtr pCell)
virtual CellPtr GetCellUsingLocationIndex(unsigned index)
void MoveCellInLocationMap(CellPtr pCell, unsigned old_index, unsigned new_index)
PottsMesh< DIM > & rGetMesh()
virtual bool IsSiteAvailable(unsigned index, CellPtr pCell)
bool IsNodeOnBase(unsigned NodeIndex, PottsMesh< 2 > *pPottsMesh)
virtual bool IsRoomToDivide(CellPtr pParentCell, CaBasedCellPopulation< 2 > &rCellPopulation)
virtual unsigned CalculateDaughterNodeIndex(CellPtr pNewCell, CellPtr pParentCell, CaBasedCellPopulation< 2 > &rCellPopulation)
std::set< unsigned > GetVonNeumannNeighbouringNodeIndices(unsigned nodeIndex)
static RandomNumberGenerator * Instance()
unsigned randMod(unsigned base)